Help to check the rate of PCR duplicate on RNA-Seq Experiment

[amirshams84]

It would be great if you help me with the following command,
do you agree with the following upstream step before PCRduplicate
Step1: Alignment
STAR \ --runThreadN 30 \ --genomeDir $GENOME \ --sjdbGTFfile /fdb/igenomes/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf \ --sjdbOverhang 75 \ --readFilesIn AB4315-L1_HNJM2BGXC_S1_R1_001.fastq.gz \ --readFilesCommand zcat \ --outSAMtype BAM SortedByCoordinate \ --outFileNamePrefix $RESULT/AB4315-L1
Step2: Post Alignment
samtools view --threads 30 -h -F 1796 -q 30 AB4315-L1.bam | \ awk 'BEGIN{OFS=FS} {if($3 != "chrUn" && $3 !~ /chrUn/ && $3 !~ /random/) print $0 }' > AB4315-L1.filtered.sam samtools sort --threads 30 AB4315-L1.filtered.sam -O bam -o AB4315-L1.filtered.sorted.bam samtools index -@ 30 AB4315-L1.filtered.sorted.bam
Step3: BCFtools
bcftools mpileup --threads 30 \ -f /fdb/igenomes/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa \ ./AB4315-L1.filtered.sorted.bam | \ bcftools call --threads 30 --ploidy GRCh38 -mv -Ov -o ./AB4315-L1.filtered.sorted.variant.bcf

[amirshams84]

here is the PCR duplicate command
./extract_duplicates --bam ./AB4315-L1.filtered.sorted.bam --VCF ./AB4315-L1.filtered.sorted.variant.bcf --singlereads 1 > ./Result/AB4315-L1.filtered.sorted.variant.hetreads

here is the progress log:
processed 2000000 reads, useful fragments 0, filtered-reads 1999999 current read->tid 0
and the result is -nan